opforch 2.0.0__tar.gz

opforch-2.0.0/LICENSE

@@ -0,0 +1,177 @@
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opforch-2.0.0/PKG-INFO

@@ -0,0 +1,229 @@
+Metadata-Version: 2.4
+Name: opforch
+Version: 2.0.0
+Summary: PyTorch-Inspired Optimum-Path Forest Classifier
+Home-page: https://github.com/gugarosa/opforch
+Author: Gustavo de Rosa
+Author-email: gustavo.rosa@unesp.br
+License: Apache 2.0
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.19.5
+Requires-Dist: torch>=2.0.0
+Provides-Extra: tests
+Requires-Dist: coverage; extra == "tests"
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-pep8; extra == "tests"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: summary
+
+# OPForch: A PyTorch-Powered Optimum-Path Forest Classifier
+
+[![Latest release](https://img.shields.io/github/release/gugarosa/opforch.svg)](https://github.com/gugarosa/opforch/releases)
+[![Open issues](https://img.shields.io/github/issues/gugarosa/opforch.svg)](https://github.com/gugarosa/opforch/issues)
+[![License](https://img.shields.io/github/license/gugarosa/opforch.svg)](https://github.com/gugarosa/opforch/blob/master/LICENSE)
+
+## Welcome to OPForch.
+
+*Note that this implementation relies purely on the standard [LibOPF](https://github.com/jppbsi/LibOPF). Therefore, if one uses our package, please also cite the original LibOPF [authors](https://github.com/jppbsi/LibOPF/wiki/Additional-information).*
+
+OPForch is a **PyTorch-based** implementation of the Optimum-Path Forest (OPF) classifier, migrated from the original [OPFython](https://github.com/gugarosa/opfython) package. By replacing per-node Python objects with dense tensors and scalar Numba loops with batched tensor operations, OPForch delivers **massive speedups** while maintaining **zero prediction mismatches** against the reference implementation.
+
+### Key Highlights
+
+| Metric | Result |
+|--------|--------|
+| **Accuracy Parity** | 0 prediction mismatches across all 4 classifiers |
+| **Predict Speedup** | Up to **484×** faster at N=10,000 |
+| **Fit Speedup** | Up to **19×** faster at N=10,000 |
+| **Distance Matrix** | Up to **413×** faster (batched tensor vs N² scalar loop) |
+| **GPU Acceleration** | **12.7×** additional speedup on RTX 4070 for distance computation |
+| **Device Support** | CPU, CUDA, and Multi-GPU via `DeviceManager` |
+
+### Use OPForch if you need:
+
+* Graph-based classification without hyperparameter tuning
+* Deterministic training with competitive accuracy
+* GPU-accelerated distance computation and prediction
+* A drop-in replacement for OPFython with orders-of-magnitude speedups
+
+OPForch is compatible with: **Python 3.8+** and **PyTorch 2.0+**.
+
+---
+
+## Package Structure
+
+```
+opforch/
+├── core/
+│   ├── heap.py          # Tensor-backed binary heap
+│   ├── subgraph.py      # Dense tensor columns (13 state tensors)
+│   └── opf.py           # Abstract base (torch.save/load, device)
+├── math/
+│   ├── distance.py      # 47 batched (N,D)×(M,D)→(N,M) distance metrics
+│   ├── general.py       # Accuracy, confusion matrix, normalize, purity
+│   └── random.py        # Tensor-based random generators
+├── models/
+│   ├── supervised.py        # MST + competition + batched predict
+│   ├── knn_supervised.py    # KNN density clustering + k-selection
+│   ├── semi_supervised.py   # Labeled + unlabeled propagation
+│   └── unsupervised.py      # Density clustering + normalized cut
+├── stream/
+│   ├── loader.py        # CSV/TXT/JSON → torch.Tensor
+│   ├── parser.py        # Extract features + labels
+│   └── splitter.py      # Train/test split
+├── subgraphs/
+│   └── knn.py           # KNNSubgraph (torch.topk, vectorized PDF)
+├── utils/
+│   ├── constants.py     # EPSILON, FLOAT_MAX, status codes
+│   ├── converter.py     # Binary OPF format converters
+│   ├── device.py        # DeviceManager (CPU/GPU/multi-GPU)
+│   ├── exception.py     # Custom exception hierarchy
+│   └── logging.py       # Timed rotating file logger
+├── report/              # Migration report, benchmarks, and plots
+├── examples/            # Usage scripts for all 4 classifiers
+```
+
+---
+
+## Installation
+
+Install from source:
+
+```bash
+git clone https://github.com/gugarosa/opforch.git
+cd opforch
+pip install -e .
+```
+
+For GPU support, install PyTorch with CUDA:
+
+```bash
+pip install torch --index-url https://download.pytorch.org/whl/cu124
+```
+
+---
+
+## Quick Start
+
+### Supervised Classification
+
+```python
+import torch
+from opforch.models import SupervisedOPF
+from opforch.stream import loader, parser, splitter
+
+# Load data
+data = loader.load_txt("data/boat.txt")
+X, Y = parser.parse_loader(data)
+X_train, X_test, Y_train, Y_test = splitter.split(X, Y, percentage=0.5)
+
+# Train and predict (CPU)
+opf = SupervisedOPF(distance="log_squared_euclidean")
+opf.fit(X_train, Y_train)
+predictions = opf.predict(X_test)
+
+# GPU — just change the device
+opf_gpu = SupervisedOPF(distance="euclidean", device="cuda:0")
+opf_gpu.fit(X_train.cuda(), Y_train.cuda())
+predictions = opf_gpu.predict(X_test.cuda())
+```
+
+### Available Classifiers
+
+| Classifier | Description |
+|-----------|-------------|
+| `SupervisedOPF` | MST-based prototype detection + cost competition |
+| `KNNSupervisedOPF` | k-NN density clustering with validation-driven k |
+| `SemiSupervisedOPF` | Extends supervised with unlabeled data propagation |
+| `UnsupervisedOPF` | Density-based clustering with normalized cut |
+
+All classifiers support `fit()`, `predict()`, `save()`, and `load()`, and accept a `device` parameter for CPU/GPU execution.
+
+---
+
+## Benchmarks
+
+Run the benchmark suite to compare performance on your hardware:
+
+```bash
+# Baseline benchmarks (47 metrics, 4 models, scaling)
+python report/benchmark.py
+
+# Extended benchmarks (up to N=10K, GPU, dimensionality)
+python report/benchmark_extended.py
+
+# Generate plots
+python report/plot_benchmarks.py
+python report/plot_extended.py
+```
+
+For the full migration report with detailed analysis, see [`report/REPORT.md`](report/REPORT.md).
+
+---
+
+## Architecture
+
+The key architectural change from OPFython is the elimination of per-node Python objects in favor of dense tensor columns:
+
+```
+OPFython:  subgraph.nodes[i].cost = 5.0        # Python object attribute
+OPForch:   subgraph.costs[i] = 5.0             # Tensor element (GPU-ready)
+```
+
+Prediction is fully batched — a single tensor operation replaces the O(N×M) Python loop:
+
+```python
+dist_matrix = distance_fn(train_features, test_features)      # (N, M)
+path_costs = torch.maximum(train_costs[:, None], dist_matrix)  # (N, M)
+predictions = train_labels[path_costs.argmin(dim=0)]           # (M,)
+```
+
+For the complete architecture documentation, see [`ARCHITECTURE.md`](ARCHITECTURE.md).
+
+---
+
+## Citation
+
+If you use OPForch to fulfill any of your needs, please cite us:
+
+```
+J. P. Papa, A. X. Falcão and C. T. N. Suzuki.
+Supervised Pattern Classification based on Optimum-Path Forest.
+International Journal of Imaging Systems and Technology (2009).
+```
+
+---
+
+## Datasets
+
+Looking for datasets? We have some pre-loaded into OPF file format in the `data/` directory. More are available at [recogna.tech](http://recogna.tech).
+
+---
+
+## Support
+
+If you ever need to report a bug, talk to us, or suggest improvements, please open an issue. We will do our best to help.
+
+---

opforch-2.0.0/README.md

@@ -0,0 +1,189 @@
+# OPForch: A PyTorch-Powered Optimum-Path Forest Classifier
+
+[![Latest release](https://img.shields.io/github/release/gugarosa/opforch.svg)](https://github.com/gugarosa/opforch/releases)
+[![Open issues](https://img.shields.io/github/issues/gugarosa/opforch.svg)](https://github.com/gugarosa/opforch/issues)
+[![License](https://img.shields.io/github/license/gugarosa/opforch.svg)](https://github.com/gugarosa/opforch/blob/master/LICENSE)
+
+## Welcome to OPForch.
+
+*Note that this implementation relies purely on the standard [LibOPF](https://github.com/jppbsi/LibOPF). Therefore, if one uses our package, please also cite the original LibOPF [authors](https://github.com/jppbsi/LibOPF/wiki/Additional-information).*
+
+OPForch is a **PyTorch-based** implementation of the Optimum-Path Forest (OPF) classifier, migrated from the original [OPFython](https://github.com/gugarosa/opfython) package. By replacing per-node Python objects with dense tensors and scalar Numba loops with batched tensor operations, OPForch delivers **massive speedups** while maintaining **zero prediction mismatches** against the reference implementation.
+
+### Key Highlights
+
+| Metric | Result |
+|--------|--------|
+| **Accuracy Parity** | 0 prediction mismatches across all 4 classifiers |
+| **Predict Speedup** | Up to **484×** faster at N=10,000 |
+| **Fit Speedup** | Up to **19×** faster at N=10,000 |
+| **Distance Matrix** | Up to **413×** faster (batched tensor vs N² scalar loop) |
+| **GPU Acceleration** | **12.7×** additional speedup on RTX 4070 for distance computation |
+| **Device Support** | CPU, CUDA, and Multi-GPU via `DeviceManager` |
+
+### Use OPForch if you need:
+
+* Graph-based classification without hyperparameter tuning
+* Deterministic training with competitive accuracy
+* GPU-accelerated distance computation and prediction
+* A drop-in replacement for OPFython with orders-of-magnitude speedups
+
+OPForch is compatible with: **Python 3.8+** and **PyTorch 2.0+**.
+
+---
+
+## Package Structure
+
+```
+opforch/
+├── core/
+│   ├── heap.py          # Tensor-backed binary heap
+│   ├── subgraph.py      # Dense tensor columns (13 state tensors)
+│   └── opf.py           # Abstract base (torch.save/load, device)
+├── math/
+│   ├── distance.py      # 47 batched (N,D)×(M,D)→(N,M) distance metrics
+│   ├── general.py       # Accuracy, confusion matrix, normalize, purity
+│   └── random.py        # Tensor-based random generators
+├── models/
+│   ├── supervised.py        # MST + competition + batched predict
+│   ├── knn_supervised.py    # KNN density clustering + k-selection
+│   ├── semi_supervised.py   # Labeled + unlabeled propagation
+│   └── unsupervised.py      # Density clustering + normalized cut
+├── stream/
+│   ├── loader.py        # CSV/TXT/JSON → torch.Tensor
+│   ├── parser.py        # Extract features + labels
+│   └── splitter.py      # Train/test split
+├── subgraphs/
+│   └── knn.py           # KNNSubgraph (torch.topk, vectorized PDF)
+├── utils/
+│   ├── constants.py     # EPSILON, FLOAT_MAX, status codes
+│   ├── converter.py     # Binary OPF format converters
+│   ├── device.py        # DeviceManager (CPU/GPU/multi-GPU)
+│   ├── exception.py     # Custom exception hierarchy
+│   └── logging.py       # Timed rotating file logger
+├── report/              # Migration report, benchmarks, and plots
+├── examples/            # Usage scripts for all 4 classifiers
+```
+
+---
+
+## Installation
+
+Install from source:
+
+```bash
+git clone https://github.com/gugarosa/opforch.git
+cd opforch
+pip install -e .
+```
+
+For GPU support, install PyTorch with CUDA:
+
+```bash
+pip install torch --index-url https://download.pytorch.org/whl/cu124
+```
+
+---
+
+## Quick Start
+
+### Supervised Classification
+
+```python
+import torch
+from opforch.models import SupervisedOPF
+from opforch.stream import loader, parser, splitter
+
+# Load data
+data = loader.load_txt("data/boat.txt")
+X, Y = parser.parse_loader(data)
+X_train, X_test, Y_train, Y_test = splitter.split(X, Y, percentage=0.5)
+
+# Train and predict (CPU)
+opf = SupervisedOPF(distance="log_squared_euclidean")
+opf.fit(X_train, Y_train)
+predictions = opf.predict(X_test)
+
+# GPU — just change the device
+opf_gpu = SupervisedOPF(distance="euclidean", device="cuda:0")
+opf_gpu.fit(X_train.cuda(), Y_train.cuda())
+predictions = opf_gpu.predict(X_test.cuda())
+```
+
+### Available Classifiers
+
+| Classifier | Description |
+|-----------|-------------|
+| `SupervisedOPF` | MST-based prototype detection + cost competition |
+| `KNNSupervisedOPF` | k-NN density clustering with validation-driven k |
+| `SemiSupervisedOPF` | Extends supervised with unlabeled data propagation |
+| `UnsupervisedOPF` | Density-based clustering with normalized cut |
+
+All classifiers support `fit()`, `predict()`, `save()`, and `load()`, and accept a `device` parameter for CPU/GPU execution.
+
+---
+
+## Benchmarks
+
+Run the benchmark suite to compare performance on your hardware:
+
+```bash
+# Baseline benchmarks (47 metrics, 4 models, scaling)
+python report/benchmark.py
+
+# Extended benchmarks (up to N=10K, GPU, dimensionality)
+python report/benchmark_extended.py
+
+# Generate plots
+python report/plot_benchmarks.py
+python report/plot_extended.py
+```
+
+For the full migration report with detailed analysis, see [`report/REPORT.md`](report/REPORT.md).
+
+---
+
+## Architecture
+
+The key architectural change from OPFython is the elimination of per-node Python objects in favor of dense tensor columns:
+
+```
+OPFython:  subgraph.nodes[i].cost = 5.0        # Python object attribute
+OPForch:   subgraph.costs[i] = 5.0             # Tensor element (GPU-ready)
+```
+
+Prediction is fully batched — a single tensor operation replaces the O(N×M) Python loop:
+
+```python
+dist_matrix = distance_fn(train_features, test_features)      # (N, M)
+path_costs = torch.maximum(train_costs[:, None], dist_matrix)  # (N, M)
+predictions = train_labels[path_costs.argmin(dim=0)]           # (M,)
+```
+
+For the complete architecture documentation, see [`ARCHITECTURE.md`](ARCHITECTURE.md).
+
+---
+
+## Citation
+
+If you use OPForch to fulfill any of your needs, please cite us:
+
+```
+J. P. Papa, A. X. Falcão and C. T. N. Suzuki.
+Supervised Pattern Classification based on Optimum-Path Forest.
+International Journal of Imaging Systems and Technology (2009).
+```
+
+---
+
+## Datasets
+
+Looking for datasets? We have some pre-loaded into OPF file format in the `data/` directory. More are available at [recogna.tech](http://recogna.tech).
+
+---
+
+## Support
+
+If you ever need to report a bug, talk to us, or suggest improvements, please open an issue. We will do our best to help.
+
+---

opforch-2.0.0/opforch/__init__.py

@@ -0,0 +1,7 @@
+"""OPForch: PyTorch-Inspired Optimum-Path Forest Classifier.
+
+This library provides GPU-accelerated OPF classifiers
+using PyTorch tensors as the universal data representation.
+"""
+
+__version__ = "2.0.0"

opforch-2.0.0/opforch/core/__init__.py

@@ -0,0 +1,5 @@
+"""Core structures for OPForch implementations."""
+
+from opforch.core.heap import Heap
+from opforch.core.subgraph import Subgraph
+from opforch.core.opf import OPF